--- a/dexseq_count.xml	Thu Oct 08 16:52:01 2015 -0400
+++ b/dexseq_count.xml	Sun Jan 29 06:59:35 2017 -0500
@@ -1,9 +1,8 @@
-<tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
+<tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="1.14">dexseq</requirement>
-        <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
+        <requirement type="package" version="0.6.1.post1">htseq</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -16,20 +15,20 @@
     <command>
     <![CDATA[
         #if $mode.mode_select == "prepare":
-            python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py
+            dexseq_prepare_annotation.py
                 -r $mode.aggregate
-                $mode.gtffile
-                $flattened_gtf_out
+                '$mode.gtffile'
+                '$flattened_gtf_out'
         #elif $mode.mode_select == "count":
-            python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py
+            dexseq_count.py
                 -f bam
                 -p $mode.paired
                 -s $mode.stranded
                 -a $mode.qual
                 -r $mode.order
                 $mode.flattened_gtf_in
-                $mode.bamfile
-                $counts_file
+                '$mode.bamfile'
+                '$counts_file'
         #end if
     ]]>
     </command>
@@ -42,7 +41,7 @@
             <when value="prepare">
                 <param name="gtffile" type="data" format="gff" label="GTF file"/>
                 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
-                    label="Aggretare genes with exons?"
+                    label="Aggregate genes with exons?"
                     help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/>
             </when>
             <when value="count">
@@ -85,7 +84,7 @@
     <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting.